This
case tests the limits of a federal court to require an agency
of the executive branch to do something that it is has
decided not to do, no matter how compelling might be the
circumstances. Plaintiffs Conservation Law Foundation, Inc.,
and Charles River Watershed Association, Inc., brought this
citizen suit under the Clean Water Act (CWA) against the
Environmental Protection Agency (EPA), the EPA's Region 1
Office, Gina McCarthy (EPA's Administrator at the time
the lawsuit was filed), and H. Curtis Spalding (the Regional
Administrator of the EPA's Region 1 Office), contending
that the EPA[1] has abdicated a nondiscretionary duty to
require stormwater dischargers along the Charles River to
apply for pollution discharge permits. The EPA now moves to
dismiss the Complaint for lack of subject matter jurisdiction
and failure to state a claim. Fed.R.Civ.P. 12(b)(1), (6).
After a hearing on the motion to dismiss, plaintiffs moved to
amend the Complaint, seeking to add a claim that the EPA has
failed to respond to a petition that plaintiffs filed in 2013
seeking designation of a number of stormwater point sources.
The EPA opposes the motion, chiefly contending that amendment
would be futile.

BACKGROUND

The
relevant facts are largely undisputed, but the parties
vigorously disagree over their fit in the overarching
regulatory framework. Under the CWA, each state is required
to set water quality standards for bodies of water within its
boundaries. 33 U.S.C. § 1313(c). Once these standards
are defined, the state determines which water bodies do not
meet the quality standards for each of a list of pollutants.
Id. § 1313(d)(1)(A). If a pollutant exceeds the
acceptable level, the state must then establish the
“total maximum daily load” (TMDL) of the
pollutant that the water body can absorb and still meet water
quality standards. Id. § 1313(d)(1)(C).

TMDLs
allocate the daily load between point sources (such as a pipe
or ditch, id. § 1362(14)) and all other
sources, creatively referred to as nonpoint sources. A TMDL
is the sum of acceptable “wasteload allocations”
from point sources and “load allocations” from
nonpoint sources. 40 C.F.R. § 130.2(g)-(i). Once a TMDL
is designed, it is submitted to the EPA for approval. 33
U.S.C. § 1313(d)(2).

A
separate section of the CWA establishes a permitting system
for the discharge of pollutants from point sources. 33 U.S.C.
§§ 1311(a), 1342(a). Under the National Pollutant
Discharge Elimination System (NPDES), dischargers must obtain
a permit that, among other restrictions, limits the quantity
and type of pollutants that can be discharged into a
protected body of water. 40 C.F.R. § 122.1(b). These
limits must be “consistent with the assumptions and
requirements of any available wasteload allocation for the
discharge” set by the relevant TMDL. Id.
§ 122.44(d)(1)(vii)(B).

Point
sources of stormwater discharges, however, are not treated
like the mine-run of point sources. Instead, they are subject
to special permitting rules established by a 1987 amendment
to the CWA. Under the 1987 amendment, only certain types of
stormwater discharge require a permit, most notably those
associated with industrial activity and municipal sewer
systems. 33 U.S.C. § 1342(p)(2). The amendment also gave
the EPA the authority to identify and regulate other sources
of stormwater discharge. Id. § 1342(p)(6).
Exercising this authority, the EPA added two types of
stormwater discharges to the NPDES permitting system, 40
C.F.R. § 122.26(a)(9)(i)(A), (B), and instituted an ad
hoc procedure for permitting where: (1) the EPA[2] “determines
that storm water controls are needed for the discharge based
on wasteload allocations that are part of ‘total
maximum daily loads' (TMDLs) that address the
pollutant(s) of concern”; or (2) where the EPA
“determines that the discharge, or category of
discharges within a geographic area, contributes to a
violation of a water quality standard or is a significant
contributor of pollutants to waters of the United
States.” Id. § 122.26(a)(9)(i)(C), (D).
These provisions make up the EPA's “residual
designation authority” (RDA).

Plaintiffs
contend that under the RDA, the EPA is required to take
urgent action to address stormwater discharges into the
Charles River. Plaintiffs point to three Charles River TMDLs
approved by the EPA in recent years. The first two TMDLs
address “nutrient” pollution in the Charles.
These TMDLs divide the Charles into two stretches: the
Upper/Middle Charles (flowing from Hopkinton to the Watertown
Dam), and the Lower Charles (flowing from the Watertown Dam
to the New Charles River Dam).

In both
stretches, nutrient pollution (primarily from phosphorus) has
fostered “cultural” or “accelerated
eutrophication, ” a process by which a body of water
produces overabundant plant life, including toxic algae,
thereby degrading water quality and deterring recreational
use. Defs.' Ex. 1, Dkt. #22-2, at 5-6, 19-20; Defs.'
Ex. 2, Dkt. # 22-3, at 2, 13-14. Both TMDLs identify
stormwater as a major source of nutrient discharge into the
Charles. Defs.' Ex. 1 at 43; Defs.' Ex. 2 at 46-51.

The
third TMDL addresses pathogen pollution, including bacteria
such as fecal coliform and E. coli. Pathogens
endanger the health of persons who drink or are otherwise
exposed to the polluted water. Defs.' Ex. 3, Dkt. #22-4,
at 3. The TMDL identifies stormwater as a major source of
pathogens, primarily because it washes animal waste and other
pathogen hosts into the Charles. Id. at 39.

All
three TMDLs and the recitations in plaintiffs' Complaint
identify significant threats to the vitality of the Charles -
the amelioration of which will require severe reductions in
the levels of nutrient and pathogen pollution contributed to
the River by stormwater. Nutrient pollution has caused toxic
algal blooms in the Charles, leading state and local
authorities to warn citizens and their pets to avoid any
contact with River water. Am. Compl. ¶¶ 48, 81.
Plaintiffs also note that high levels of pathogen pollution
have forced the cancellation of public swimming events. Am.
Compl. ¶ 52. The Lower Charles nutrient TMDL
implementation plan will require “Commercial, ”
“Industrial, ” and “High Density
Residential” land users to reduce phosphorous loading
by 65% from 1998-2002 levels, while cities and towns along
the Charles will be required to achieve reductions in excess
of 60% of 1998-2002 levels. Defs.' Ex. 1 at 106-112. The
implementation plan for the Upper/Middle Charles nutrient
TMDL also calls for severe reductions in nutrient
contributions by
“Commercial/Industrial/Transportation” and
“High Density/Medium Density/Multi-Family
Residential” land users on “the same [scale] as
those called for in the Lower Charles Nutrient TMDL.”
Defs.' Ex. 2 at 84. The pathogen TMDL, for its part,
envisions reductions of 41.2%-98.8% in bacteria loading and
reductions of 97.1%-97.6% in fecal coliform loading for
comparable land use categories. Defs.' Ex. 3 at 40.

Plaintiffs
filed this lawsuit on February 25, 2016, and amended the
Complaint on June 20, 2016. The court heard oral argument on
the EPA's motion to dismiss on February 3, 2017. At the
conclusion of the argument, the court invited additional
comments concerning the relationship between this suit and
the citizen petition provision of the EPA's regulations
implementing the RDA. See 40 C.F.R. §
122.26(f)(2). Both parties responded, and plaintiffs,
together with their response, sought leave to add an
additional count to the Complaint. That count would assert
that the EPA has failed to fulfill the nondiscretionary duty
imposed under the RDA to make a final determination on
citizen petitions for point source designations within 90
days of receipt. See Id. § 122.26(f)(5).
Specifically, plaintiffs contend that the EPA has yet to
issue a final determination on a petition filed on July 10,
2013, requesting the EPA to require permits for commercial,
industrial, and institutional stormwater discharges at some
1, 711 locations in New England.

DISCUSSION

Relying
on the citizen suit provision of the CWA, 33 U.S.C. §
1365, plaintiffs allege that the EPA has failed under 40
C.F.R. § 124.52 to distribute NPDES permit applications
to various commercial, industrial, institutional, and
high-density residential stormwater point sources along the
Charles (the EPA does not contest the fact that it has not
done so). The essence of plaintiffs' argument is that the
EPA, in approving the Charles ...

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